Khalfan Mohamed allegedly received training in Afghanistan. It is believed that Mohamed assembled the bomb used against the embassy in the Dar es Salaam, Tanzania, and flew to South Africa shortly after the bombing. He was arrested in Cape Town on October 5, 1999, after he was discovered to still be using the same alias he had used during the bombings.[3] After interrogation, South African immigration authorities handed him over to FBI agents and he was flown to New York on the following day.[4] (This extradition subsequently became the subject of a landmark decision of the Constitutional Court of South Africa, Mohamed v President of the Republic of South Africa, which determined that the South African government cannot extradite suspects who may face the death penalty.)

In 2014, he successfully sued the US government for violating his Freedom of Speech by prohibiting his communications with all but a few immediate family members.[citation needed]

On November 2, 2000, Mohamed and Mamdouh Mahmud Salim (also of al-Qaeda) attacked a federal prison guard in a failed escape attempt. The officer was critically injured, having been stabbed in the eye with a sharpened comb, and suffered severe brain damage from the attack.[5] During the sentencing phase of his trial, prosecutors argued unsuccessfully for capital punishment of Mohamed, due to the continuing threat he posed to prison guards.[5]